US20100292101A1 - Method and apparatus for the analysis and identification of molecules - Google Patents

Method and apparatus for the analysis and identification of molecules Download PDF

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US20100292101A1
US20100292101A1 US12/777,151 US77715110A US2010292101A1 US 20100292101 A1 US20100292101 A1 US 20100292101A1 US 77715110 A US77715110 A US 77715110A US 2010292101 A1 US2010292101 A1 US 2010292101A1
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nanopore
wafer
plurality
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Daniel Wai-Cheong So
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Genvida Technology Co Ltd
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    • B01L3/5027Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
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Abstract

An apparatus and method for performing analysis and identification of molecules have been presented. In one embodiment, a portable molecule analyzer includes a sample input/output connection to receive a sample, a nanopore-based sequencing chip to perform analysis on the sample substantially in real-time, and an output interface to output result of the analysis.

Description

    RELATED APPLICATION
  • This application claims the benefit of U.S. Provisional Patent Application No. 61/177,553, filed May 12, 2009, which is herein incorporated by reference in its entirety.
  • TECHNICAL FIELD
  • The present invention relates generally to analyze and identify of molecules, and in particular to providing a real-time, portable, nanopore-based molecule analysis apparatus.
  • BACKGROUND
  • Nucleic acids, deoxyribonucleic acid (DNA), and/or ribose nucleic acid (RNA) are present and have unique sequences in every living organism. It lends itself naturally as a definitive identification for various bio-agents. Therefore, analysis of nucleic acids, DNA, and/or RNA, which is broadly referred to as genomic analysis herein, is very useful in studying living organisms. However, the currently commercially available nucleic acid sequencing technologies, such as microarray, pyrosequencing, sequencing by synthesis and sequencing by ligation are very limited in various aspects. For instance, some or all of these technologies cannot perform real-time analysis, require lengthy sample nucleic acid amplification procedures and protocols (such as polymerase chain reaction), have long turnaround time (typically takes about several days to weeks to analyze a small fragment of the sample nucleic acid), have high operation cost (some of which use expensive chemical reagents), have high false-positive error rates, and are non-portable.
  • Because of the above limitations of the current nucleic acid sequencing technologies, people working in the fields, such as medical professionals, security personnel, scientists, etc., cannot perform genomic analysis on-site locally. Rather, field workers have to collect and transport samples to specialized laboratories to be analyzed for days, or even weeks, in order to identify the nucleic acids present in the sample. Such lengthy tedious process can hardly meet today's need for genomic analysis, especially during epidemic outbreaks, such as the foot-and-mouth epidemic in United Kingdom, the Severe Acute Respiratory Syndrome (SARS) outbreak in Asia, and the recent H1N1 flu (also commonly known as swine flu) outbreak in Mexico and the United States. Using the current nucleic acid sequencing technologies, it is difficult, if not impossible, for the authorities to formulate a swift and informed decision, which could have an enormous safety and economic impact on the society.
  • To address the shortfalls of the above nucleic acid sequencing technologies, scientists have developed various nanopore-based sequencing technologies. Recently, Professor Hagan Bayley of Oxford University and his co-workers demonstrated long read with 99.8% accuracy using the α-haemolysin in a bio-nanopore experiment. Based on the established detection speed, an array of 256×256 nanopores is generally sufficient to analyze the human genome in its entirety within about thirty minutes. This would be a watershed triumph if one can successfully realize the bio-nanopore array. However, one drawback for bio-nanopores is the relative short lifetime, typically several hours to days, of the proteins and enzymes used in forming the bio-nanopores.
  • Solid state nanopore is a more robust alternative to bio-nanopore since there is no bio-reagent involved in the construction of the solid state nanopores. However, conventional lithography technologies employed in semiconductor industry are not capable of defining the 2-nm feature size required by the solid-state nanopore-based sequencing technologies. Thus far, different fabrication techniques, for instance, electron/ion milling, have been used to sequentially carve the nanopores one at a time. But these techniques cannot be scaled to produce the 256×256 array with affordable cost and reasonable production time.
  • BRIEF DESCRIPTION OF THE DRAWINGS
  • The present invention is illustrated by way of example, and not of limitation, in the figures of the accompanying drawings in which:
  • FIG. 1 illustrates one embodiment of a nanopore-based sequencer and an associated nanopore-based sequencing biochip;
  • FIG. 2A illustrates one embodiment of a translocation process of a molecule during the detection and analysis of nanopore based nucleic acid sequencing;
  • FIG. 2B illustrates a corresponding exemplary electrical readout of the nucleic acid sequence as compared with the background signal of an empty pore;
  • FIG. 3 illustrates a side view and a top view of one embodiment of an Einzel lens used in the nanopantography for both etch and deposition;
  • FIGS. 4A-4E illustrate one embodiment of an subtractive method for fabricating a nanopore and/or a nanopore array;
  • FIGS. 5A-5I illustrate one embodiment of a additive method for fabricating a nanopore and/or a nanopore array;
  • FIG. 6 illustrates one embodiment of a nanoring and one embodiment of a nanoslit;
  • FIG. 7 illustrates one embodiment of a bonded nanopore array wafer and integrated circuit wafer to form the bottom cavity of a measurement chamber;
  • FIG. 8 illustrates one embodiment of a bonded top wafer and composite wafer to form the top cavity of the measurement chamber;
  • FIG. 9 illustrates one embodiment of a voltage biasing scheme and current sensing circuit operable with a nanopore-based sequencer;
  • FIG. 10A illustrates one embodiment of a nanopore-based sequencer;
  • FIG. 10B illustrates one embodiment of multiple measurement chambers;
  • FIG. 11 illustrates a cross-sectional view of one embodiment of a nanopore-based sequencer along a selected path from the sample intake, along the microfluidic channel and the nanofluidic channel, through the measurement chamber, then to the sample outlet;
  • FIG. 12 illustrates one embodiment of a trilayer biochip structure with embedded electrodes;
  • FIG. 13A illustrates one embodiment of a biasing and sensing scheme for nanopore detection;
  • FIG. 13B illustrates one embodiment of a planar electrode implementation;
  • FIG. 13C illustrates a top view of one embodiment of sensing electrodes and nanoslit in planar electrode implementation;
  • FIG. 14 illustrates a high-level hardware architecture of one embodiment of a nanopore-based sequencer; and
  • FIG. 15 illustrates a high-level architecture of the software and related hardware components for the operating system and the genomic analysis software in one embodiment of a nanopore-based sequencer.
  • DETAILED DESCRIPTION
  • In the following description, numerous specific details are set forth such as examples of specific components, devices, methods, etc., in order to provide a thorough understanding of embodiments of the present invention. It will be apparent, however, to one skilled in the art that these specific details need not be employed to practice embodiments of the present invention. In other instances, well-known materials or methods have not been described in detail in order to avoid unnecessarily obscuring embodiments of the present invention.
  • Various embodiments of an apparatus and a method to perform analysis and identification of molecules, such as, nucleic acids, amino acids, peptides, proteins and polymers, and nanometer sized particles, such as carbon nanotubes, silicon nanorods and coated/uncoated gold nanoparticles, are described below. Note that the following discussion is focus on one example of molecule analysis, namely genomic analysis, in order to illustrate the concept. One of skilled in the art would readily recognize that the technique disclosed herein is applicable to analyze and identify molecules in general. In one embodiment, a nanopore-based sequencer is a portable genomic analysis system. FIG. 1 illustrates one embodiment of a portable nanopore-based sequencer 110 and an associated nanopore-based sequencing biochip 120. During detection and analysis, a molecule in a sample under test is electrophoretically driven in solution through a nano-scale pore (also referred to as a nanopore), as illustrated in FIG. 2A. In some embodiments, the size of the nanopore is about 2 nm. Note that the size of the nanopores may vary in different embodiments. For example, the nanopores are of fixed identical size in some embodiments. In some alternate embodiments, the nanopores are of different sizes. Furthermore, the shape of the nanopores may also vary in the same embodiment, or in different embodiments, such as circles, ovals, elongated slits, etc. Contingent upon the relative size and travelling speed of the molecule in the space confined within the nanopore, various electrical characteristics, such as current pulses of different amplitudes and durations, as represented in FIG. 2B, can be observed and utilized to identify the molecule. As a result, direct read of the nucleic acid sequence can be achieved without destroying the molecule under test. In other words, measurements can be made on the nucleic acid sequence while keeping the nucleic acid sequence intact.
  • Multiple fabrication techniques may be utilized to massively produce the nanopore array, which includes an array of about 2-nm pores in some embodiments, without fundamental limitations. Details of some exemplary fabrication techniques are discussed in details below to illustrate the concept. One of skill in the art would appreciate that other comparable fabrication techniques or variations to these techniques may be adopted to produce the nanopore array. By incorporating into a network of micro-/nano-fluidic channels, the nanopore-based sequencer can accurately decipher the genome with unprecedented speed and without human intervention.
  • Besides the small form-factor and speed in genomic analysis, some embodiments of the nanopore-based sequencer offer the following additional advantages. One of the advantages is ready production of future proof to any mutations in the bio-agents. This is possible because nanopore-based sequencing is a direct read technique whose results do not require prior knowledge of the genome under test. Furthermore, some embodiments of the nanopore-based sequencer are operable in extreme conditions and unclean environment because sterility and cleanliness are always ensured for the nanopores as the nanopores are always enclosed inside the nanopore-based sequencing biochip and are not exposed to any unwanted foreign substances during the entire analysis process.
  • As a handheld portable device, some embodiments of the nanopore-based sequencer can accelerate the advancement in many different industries and science. For instance, in commerce as well as research and development, some embodiments of the nanopore-based sequencer may be useful in basic research, pharmacogenomics, bacterial diagnostics, pathogen detection, agriculture, food industries, biofuel, etc. As further examples, some embodiments of the nanopore-based sequencer may be useful in rapid DNA forensics, port-of-entry bio-screening, etc.
  • Nanopore Array for Nanopore-Based Sequencing
  • In the 1970s, based on the resistive-pulse technique of the Coulter Counter, DeBlois and colleagues successfully demonstrated the use of single submicron diameter pores in characterizing particles by their sizes and electrophoretic mobility. Subsequently, Deamer proposed the idea of using nanometer sized pores for gene sequencing. He and his colleagues demonstrated that single-stranded DNA (ssDNA) and RNA molecules can be driven through a pore-forming protein and detected by their effect on the ionic current through this nanopore. Given the recently demonstrated high sequencing speed, the progress of nanopore-based sequencing is largely hampered by the lack of an inexpensive and parallel-write fabrication process to create a large array of nanopores for rapid genomic analysis. Many of the conventional lithography methods, electron milling, ion milling, and silicon etch back are not viable means to manufacture the nanopore array required for real-time genomic analysis. Until recently, Donnelly and colleagues in the University of Houston developed some embodiments of nanopantography that can massively produce 2-nm nanopore arrays without much limitations. According to their simulation results, nanopantography is capable of defining holes or dots with size as small as 1-nm. By incorporating the technologies of micro-/nano-fluidics, nanopantography opens up the possibility of achieving real-time or near real-time genomic analysis systems.
  • In nanopantography, a broad, collimated, monoenergetic ion beam is directed at an array of submicron-diameter electrostatic lenses (also referred to as Einzel lenses, as shown in FIG. 3) fabricated on the conductive substrate, e.g., doped silicon (Si) wafer. By applying appropriate voltages to the lens electrodes, the “beamlets” entering the lenses are focused to spots that can be 100 times smaller than the diameters of the lenses. This means a 1-nm feature can be defined by a 100-nm lens, which can be handled by the photolithographic techniques used in present semiconductor processing. Also, each lens writes its own nanometer feature on the substrate, therefore, nanopantography is a parallel-write process, very different from the sequential writing of the focused electron beam or ion beam. Because the lens array is part of the substrate, the method is substantially immune to misalignment caused by vibrations or thermal expansion. The size of the nanometer features is controlled by the size of the pre-defined lenses, whose diameters could be identical or different, i.e., an array of identical or different nanometer features can be processed substantially simultaneously. With an Ar+ beam in the presence of Cl2 gas, 10-nm diameter, 100-nm deep etched Si holes have been demonstrated. Etching may occur only in the holes for which a voltage is applied to the top metal layer so that the ion beamlets are focused. The rest of the holes will have no voltage applied to the top metal layer, the beamlets will not be focused, and the current density will be too small to cause any appreciable etching.
  • With the nanopantography, there are two methods, namely the subtractive method and the additive method, to fabricate the nanopores for genomic analysis. One embodiment of a direct etch method is first discussed below, and then followed by discussion of one embodiment of an indirect etch method.
  • A. One Embodiment of a Subtractive Method for Fabricating Nanopores and/or Nanopore Array
  • FIGS. 4A-4E illustrate one embodiment of a subtractive method for fabricating a nanopore and/or a nanopore array. Referring to FIG. 4A, nitride 420 is deposited on a Si (100) wafer 410. In FIG. 4B, the bottom conducting material 422, doped silicon or metal, is deposited, followed by the dielectric spacer 424, and the top metal layer 426. Then a number of Einzel lenses are defined. Referring to FIG. 4C, the nanopantographic etch is performed on the conducting material 422 to define the nanometer holes 430, which are used as hardmask for the nanopore etch in the nitride layer 420. In FIG. 4D, the Einzel lenses are removed. Then the nanopores 430 are coated with oxide 435 for protection. Finally, in FIG. 4E, the bottom cavity 440 of the measurement chamber is formed by chemical mechanical polishing (CMP), lithographic technique and potassium hydroxide (KOH) etch on the backside of the silicon substrate 410. The oxide layer 435 is then removed to reveal the nanopores 430.
  • B. One Embodiment of a Additive Method for Fabricating Nanopore and/or Nanopore Array
  • FIGS. 5A-5I illustrate one embodiment of an additive method for fabricating a nanopore and/or a nanopore array. Referring to FIG. 5A, nitride 520 is deposited on a Si (100) wafer 510. In FIG. 5B, the bottom conducting material 522, doped silicon or metal, the dielectric spacer 524, and the top metal layer 526 are deposited. Then the Einzel lenses are defined. In FIG. 5C, the nano-seed 530 for nanorod or nanotube growth is deposited. In FIG. 5D, the nanorod or nanotube 535 is grown. In FIG. 5E, oxide 540 is deposited. In FIG. 5F, the nanorod or nanotube 535 is removed. The remaining oxide nanometer hole 550 is used as hardmask for the conductive layer and the nitride layer. In FIG. 5G, a pattern is transferred from the oxide layer 540 to conductive layer 522, then to nitride layer 520. In FIG. 5H, the Einzel lenses are removed, followed by removal of the oxide layer 540. The nanopores are coated with oxide 552 for protection. Finally, in FIG. 5I, the bottom cavity 560 of the measurement chamber is formed by CMP, lithographic technique and KOH etch on the backside of the silicon substrate 510. The oxide layer 552 is then removed to reveal the nanopores 565.
  • FIG. 6 illustrates one embodiment of a nanoslit and one embodiment of a nanoring usable in some embodiments of the invention. The elongated nano-sized nanoslits 610 and nanorings 620 can be defined by some embodiments of the subtractive method with Einzel lenses (which is discussed above) with openings in the shape of a rectangle and a semi-circle, respectively, as depicted in FIG. 6. Based on the disclosure made herein, it should be apparent to one of skilled in the art that any two-dimensional shapes can be defined using similar patterning technique. Since the wafer stage is substantially stationary during the entire process in some embodiments, this non-circular patterning method solves at least three of the major technical issues confronted by the conventional method of tilting the wafer stage. First, there is no need for precise control of the tilting angle and speed of the wafer stage. Second, it generally overcomes the line-broadening effect and the line-width non-uniformity introduced by tilting the wafer relative to the incoming beam of ions. Third, it allows different shapes and sizes of patterns to be defined at about the same time.
  • Nanopore-Based Sequencing Biochip
  • After the nanopore array is formed with either the subtractive or additive method, the nanopore array wafer 750 can be bonded onto a wafer with pre-fabricated integrated circuits 720 and microfluidics channels 730, as shown in FIG. 7. This completes the formation of the bottom cavity of the measurement chamber. The nucleic acid sample can be extracted out of the biochip through the microfluidic channels on the bottom wafer if desired.
  • Similarly, in some embodiments, the top cavity of the measurement chamber is formed by bonding a top wafer 810 with the integrated circuit 820 and/or the fluidic channels 830 onto the composite wafer, which includes the bonded nanopore wafer 840 and the bottom wafer 850. This trilayer wafer structure 800 is illustrated in FIG. 8. One embodiment of the voltage biasing scheme 910 and the associated current sensing circuit 920 are depicted in FIG. 9. With proper fluid I/O connections, such as those with minimal dead-volume, the trilayer composite wafer 800 is then mounted on a supporting frame for wire bonding or bell grid wire bonding. Typical packaging techniques, for example, epoxy encapsulation and ceramic packaging, can be used to enclose the whole assemble to form the nanopore-based sequencing biochip. Alternatively, integrated circuits, such as those associated with sensing and biasing, may be fabricated on the nanopore wafer 840, which may be bonded to blank substrate instead of another wafer having integrated circuits thereon.
  • Furthermore, in some embodiments, there are two more features embedded on the top wafer 810, namely the sample guiding electrodes 1015 along the microfluidic channel 1010 and the nanofluidic channel 1013 leading to the measurement chamber 1030, as shown in FIGS. 10A and 11. To further illustrate the flow of sample through the nanopore-based sequencing biochip, one example is discussed in details below.
  • The buffer intake 1025 and buffer outlet 1027 are for pre-wet and pre-fill the network of microfluidic channel 1010, the nanofluidic channel 1013 and the measurement chamber 1030 before the intake of the sample for detection. During detection, the fluid flow in the microfluidic channel can be adjusted by the flow rate of the buffer intake and outlet using the on-chip or off-chip micropumps and microvalves.
  • In one example, the phosphate-deoxyribose backbone of a single strand nucleic acid molecule is charged with a negative charge for each base segment, and there are two negative charges at the 5′-end of the molecule. A positive voltage pulsating along the sample guiding electrode chain 1015 from the receptive reservoir 1020 through the sample intake connector 1023 to the destined measurement chamber 1030 can extract the nucleic acid molecule from the receptive reservoir 1020 and deliver the molecule to the pre-assigned measurement chamber 1030. Likewise, sample guiding electrodes 1017 also are embedded on the bottom wafer along the microfluidic channels 1010 for extracting the samples out of the nanopore-based sequencing biochip in a similar way.
  • Using similar scheme of sample guiding electrodes along the network of fluidic channels, one can extend the number of measurement chambers 1040 to more than one. An example of the measurement chambers arranged in a tree architecture is illustrated in FIG. 10B. Besides the ability to perform multiple independent analyses, the order of the DNA fragments as they are being extracted from the sample receptive reservoir 1020 is pre-assigned to each measurement chamber in some embodiments. As shown in FIG. 10B, the measurement chambers 1040 are labeled with a 2-digit number. The first digit denotes the branch number and the second digit indicates the position of the measurement chamber in a branch. The assignment order of the measurement chambers 1040 may simply be in the ascending order, i.e., the chamber with the lowest number can be used first and then the chamber with next higher number. In this way, all of the measurement chambers in a branch can be used before moving onto the next branch. Alternatively, the samples can be assigned to the chambers with the lowest number in each branch with the lowest branch number being used first., i.e., 11, 21, 31, 41 then 12, 22, 32, 42, so on and so forth in the current example. According to this assignment approach, the measurement chamber of each branch with the furthest distance from the central microfluidic channel may be assigned first, then the next one of each branch. This approach may reduce the interference of the electrical signal of the sample guiding electrodes in the central microfluidic channel onto the measured signals. When the overall measurement is completed, the sequence of the entire DNA sample can be systematically assembled according to the order of extraction of the fragments. This may eliminate the time consuming post detection analysis required by other conventional sequencing technologies, such as, microarray, in which the hybridization process randomizes the original sequence of the sample and a computation intensive and error-prone post-detection analysis is required to piece back the proper sequence. Furthermore, since the order of extraction of the fragments is recorded, the fragments can be recombined to form the original DNA sample. For the other conventional sequencing technologies, the original sample is typically destroyed and cannot be retrieved for future use.
  • Referring back to FIG. 10A, the nanofluidic channel 1013 formed by wafer bonding of the top and composite wafer may serve as a filter, a sample flow rate controller, as well as a molecule stretcher. In some embodiments, the nanofluidic channel serves as a filter by turning on and off the top electrode on the top wafer, one can selectively pull in the sample from the microfluidic channel. In some embodiments, the nanofluidic channel serves as a sample flow rate controller by adjusting the voltages of the top and bottom electrodes, one can control the flow rate of the sample through the nanofluidic channel. The nanofluidic channel 1013 may also serve as a molecule stretcher because the single strand nucleic acid molecule 1101 may be stretched out from the natural curl up state when it passes through the nanofluidic channel 1013, as depicted in FIG. 11.
  • In some embodiments, the speed control properties of the nanofluidic channels are exploited to allow more accurate analyses of molecules. As illustrated in FIG. 12, the sensing electrodes 1205 are embedded in the nanopore 1225, which become an integral part of the micro-/nano-channel network in controlling the flow of the molecules through the nanopore 1225. In addition to the nanofluidic channel, the applied DC voltages are designed to fine tune the speed and the direction of the molecules when translocating through the nanopore 1225. By alternating the magnitude of the DC biasing voltages applied to the top and bottom driving electrodes 1230 and 1235, respectively, and the embedded sensing electrodes 1205, the molecule under test can be drawn through the nanopore 1225 back and forth multiple times for repeated analyses, in order to increase the accuracy in identifying the molecules by eliminating the statistical error, i.e., the false-positive error rate can be reduced.
  • Unlike some conventional approach, where the sensing electrodes are integrated into the nanopore, it might only take several nanoseconds for each base in the DNA to travel through the nanopore. Such transit time is too short for any meaningful measurement. In view of this shortcoming, other conventional approaches have been developed to slow down the movement of molecules through the nanopore. One conventional approach proposes a voltage trapping scheme to control the speed of the molecules by embedding extra electrodes into the nanopore. The proposed voltage trapping scheme is difficult to implement since it requires four or more conducting electrodes stacked on top of each other and electrically insulated from each other by sandwiching dielectric material in between the conducting electrodes. The required 2-3 nm nanopore forms on this multi-layer film may have an aspect ratio of more than 30:1, which is difficult, if not impossible, to achieve with the current integrated circuit fabrication technologies.
  • As shown in FIG. 13A, the applied AC sensing voltages 1310 are for interrogating the molecules while they are translocating through the nanopore 1325. Consequently, various sensing mechanisms can be employed to identify the molecule, for instance, change in resistance, change in capacitance, change in phase and/or tunnelling current. Due to the close proximity of the embedded sensing electrodes 1305 and the molecules under test, signal-to-noise ratio can be improved.
  • The above exemplary sample delivery and filtering mechanism serves as an example to illustrate how an array of nanopore measurement chambers can be implemented. One of skill in the art would recognize that variations to the above delivery and filtering mechanism may be adopted in different embodiments. Furthermore, array of pores with different sizes can be realized using the illustrated methods. Together with the protein pores, such as α-haemolysin, and the above mentioned array of solid-state nanopores, an array of bio-nanopores can also be realized. In some embodiments, both sensing electrodes may be placed onto the same conducting layer, instead of the stacked electrodes on different conducting layers described above. FIG. 13B illustrates one embodiment of this planar electrode implementation. In this planar electrode implementation, both sensing electrodes 1307 are placed on the same conducting layer, with a nanoslit 1327 defined in between the sensing electrodes 1307. A top view of the sensing electrodes 1307 and the nanoslit 1327 are illustrated in FIG. 13C. As discussed above, both nanopore and nanoslit can be defined using the nanopantography.
  • The ability to perform molecule detection substantially in real-time, the ability to perform single molecule detection without the pre-detection sample amplification, the ability to carry out multiple and substantially simultaneous detections, the ability to do multi-pass detection, the ability to identify the sample without the computation intensive post-detection analysis, and/or the ability to retain the sample after detection for future use are very crucial in providing a low cost, fast and accurate genomic analysis in some embodiments, for instance, in recognizing the single nucleotide polymorphism.
  • Nanopore-Based Sequencer
  • Nanopore-based sequencer provides a portable genomic detection and analysis system. In some embodiments, the nanopore-based sequencer includes two major components, namely hardware and software. Some embodiments of the high level architectures and subunits are discussed below.
  • A. Hardware System
  • In some embodiments, the hardware system of nanopore-based sequencer includes two major units, namely the computing, communication and control unit and the nanopore-based sequencing biochip interface unit, and various modules. One embodiment of the high level architecture is shown in FIG. 14. The details of various parts are further explained below.
  • I. Computing, Communication, and Control Unit
  • In one embodiment, the hardware system 1400 includes a portable computing system with a display device 1410. This may be implemented using a tablet, a laptop, a netbook, an all-in-one desktop computer, a smartphone, a personal digital assistant (PDA) or any handheld computing devices, etc. It serves as the central unit for running the operating system (OS), executing the data analysis software, storing data, controlling the operation of the nanopore-based sequencing biochip, and collecting data from the nanopore-based sequencing biochip.
  • In one embodiment, the hardware system 1400 further includes a network communication module 1420. The network communication module 1420 includes one or more of WiFi, WiMAX, Ethernet, Bluetooth, telephone capability, satellite link, and Global Positioning System (GPS), etc. The network communication module 1420 serves as the communication hub for communicating with the central computing system for data sharing, program update, data analysis, etc., communicating with other computing devices such that the data can be shared and the data analysis can be run in parallel in multiple computing devices, communicating with other bluetooth enabled devices (e.g., cellular telephone, printer, etc.), data sharing, program update, etc., and sending and receiving the GPS signal.
  • In one embodiment, the hardware system 1400 further includes an input device 1430. The input device 1430 may include one or more of a keyboard, a touch screen, a mouse, a trackball, infrared (IR) pointing device, and voice recognition device, etc. The input device 1430 serves as the human interface for command entry and data entry.
  • In one embodiment, the hardware system 1400 further includes an input/output (I/O) port 1440, which may include a flash memory card interface, an IEEE 1394 interface, and a Universal Serial Bus (USB) interface, etc. The I/O port 1440 serves as a serial interface with other electronic devices, a secondary data storage interface, and measurement data I/O for the nanopore-based sequencing biochip.
  • II. Nanopore-Based Sequencing Biochip Interface Unit
  • In some embodiments, a nanopore-based sequencing (nSeq) biochip interface unit 1450 couples to an nSeq electronic module 1460, a fluid control module 1470, a chemical storage and fluid I/O connection module 1480, and an nSeq fluid control and sample I/O connection module 1490. The nSeq electronic module 1460 controls the distribution of nucleic acid module, control the flow rate of the nanofluidic channels, collect measurement data, and output data to the computing, communication, and control unit.
  • In some embodiments, the fluid control module 1470 controls the fluid flow between the chemical storage and the nSeq biochip via the buffer intake/outlet connectors and the use of the on-chip or off-chip micropumps and microvalves. The chemical storage and fluid I/O connection module 1480 can supply chemical to the nSeq biochip, if needed, and can also serve as a chemical and/or bio-waste storage. The nSeq fluid control and sample I/O connection module 1490 can control the fluid and sample flow in the nSeq biochip as well as control the sample intake and outlet of the nSeq biochip. For instance, referring back to FIG. 10B, if one wants to perform detection at measurement chamber #11, the buffer outlet for branch #1 will be opened while all of the other buffer outlets are closed. As a result, the fluid will flow from the sample intake toward branch #1 and works in synchronous with the sample guiding electrodes along the microfluidic channels to deliver the sample to measurement chamber #11.
  • B. Software Architecture
  • FIG. 15 illustrates a high-level architecture of the software and related hardware components for the operating system and the genomic analysis software in one embodiment of a nanopore-based sequencer. Various logic processing modules in the software architecture shown can be implemented by processing devices (such as the portable computing system 1410 in FIG. 14) executing instructions embodied in computer-readable medium. A computer-readable medium includes any mechanism that provides (i.e., stores and/or transmits) information in a form accessible by a computer (e.g., a server, a personal computer, network device, personal digital assistant, manufacturing tool, any device with a set of one or more processors, etc.). For example, a computer-readable medium includes recordable/non-recordable media (e.g., read only memory (ROM); random access memory (RAM); magnetic disk storage media; optical storage media; flash memory devices; etc.); etc.
  • As mentioned above, an operating system 1510 is installed in the computing, communication and control unit. The operating system 1510 may include Windows, Linux, or any operating system suitable for computing devices. Aside from the operating system 1510 installed in the computing, communication and control unit, the genomic analysis software further includes five processing modules, namely, a graphical user interface (GUI) 1520, a data viewer 1530, a genomic data analyzer interface 1540, a genomic data analyzer 1550, and a genomic database 1560. Some embodiments of the interaction between the operating system 1510, the above processing modules 1520-1560, and the other hardware components are discussed below with reference to FIG. 15.
  • In some embodiments, the genomic data analyzer interface 1540 acts as a data flow control unit in the genomic analysis software architecture. After obtaining the commands and/or input data from the input device, the operating system 1510 transmits the information to the genomic data analyzer 1550 through the genomic data analyzer interface 1540. The genomic data analyzer 1550 then acts accordingly. With the proper commands (e.g., GET, ADD, etc.), the genomic data analyzer interface 1540 controls the data flow between the I/O port 1570 and the genomic database 1560, so the data stored in the database 1560 can be sent out or updated. Similarly, the analyzer software can be periodically updated via the I/O port 1570 and/or the input devices 1580. The genomic data analyzer interface 1540 is also coupled to the nSeq biochip interface 1590 to monitor the nSeq biochip. The status of the nSeq biochip is monitored and shown in a display unit (such as the display device in the portable computing system 1410 in FIG. 14) via the analyzer interface 1540. The genomic data analyzer interface 1540 also takes the results from the genomic data analyzer 1550 and shows them in the display unit.
  • In some embodiments, the genomic data analyzer 1550 is the main data analysis unit of the genomic analysis software. It obtains the measurements from the nSeq biochip, performs analysis and then compares the results with the data stored in the database 1560 to identify the bio-agents. The analysis results can be shown in the display unit and stored in the database 1560 for future reference.
  • The genomic database 1560 is a data repository for storing the existing bio-agents and newly discovered nucleic acid sequences. The data viewer 1530 includes software routines that take the data and information from some or all of the other units and show them on the display device.
  • Thus, a method and apparatus for portable real-time analysis and identification of molecules has been described. It will be apparent from the foregoing description that aspects of the present invention may be embodied, at least in part, in software. That is, the techniques may be carried out in a computer system or other data processing system in response to its processor executing sequences of instructions contained in a memory. In various embodiments, hardwired circuitry may be used in combination with software instructions to implement the present invention. Thus, the techniques are not limited to any specific combination of hardware circuitry and software or to any particular source for the instructions executed by the data processing system. In addition, throughout this description, various functions and operations may be described as being performed by or caused by software code to simplify description. However, those skilled in the art will recognize what is meant by such expressions is that the functions result from execution of the code by a processor or controller.
  • It should be appreciated that references throughout this specification to “one embodiment” or “an embodiment” means that a particular feature, structure or characteristic described in connection with the embodiment is included in at least one embodiment of the present invention. Therefore, it is emphasized and should be appreciated that two or more references to “some embodiments” or “one embodiment” or “an alternative embodiment” in various portions of this specification are not necessarily all referring to the same embodiment. Furthermore, the particular features, structures or characteristics may be combined as suitable in one or more embodiments of the invention. In addition, while the invention has been described in terms of several embodiments, those skilled in the art will recognize that the invention is not limited to the embodiments described. The embodiments of the invention can be practiced with modification and alteration within the scope of the appended claims. The specification and the drawings are thus to be regarded as illustrative instead of limiting on the invention.

Claims (22)

1. A portable molecule analyzer, comprising:
a sample input/output connector to receive a sample;
a nanopore-based sequencing chip comprising a plurality of nanopores, to measure one or more electrical characteristics of the sample substantially in real-time; and
a portable computing system to perform analysis on measurement data from the nanopore-based sequencing chip substantially in real time.
2. The portable molecule analyzer of claim 1, wherein the nanopore-based sequencing chip measures the one or more electrical characteristics of the sample while keeping molecules in the sample substantially intact.
3. The portable molecule analyzer of claim 1, further comprising:
a nanopore-based sequencing electronic control module to control a flow rate of the sample through the plurality of nanopores of the nanopore-based sequencing chip, and to send the measurement data from the nanopore-based sequencing chip to the portable computing system.
4. The portable molecule analyzer of claim 3, wherein the nanopore-based sequencing electronic control module is operable to adjust voltages applied to a plurality of driving electrodes on the nanopore-based sequencing chip to control a speed at which molecules in the sample flow through the plurality of nanopores.
5. The portable molecule analyzer of claim 3, wherein the nanopore-based sequencing electronic control module is operable to apply a set of adjustable voltages to a plurality of driving electrodes on the nanopore-based sequencing chip to cause a molecule in the sample to pass through one of the plurality of nanopores multiple times.
6. The portable molecule analyzer of claim 1, wherein the one or more electrical characteristics comprise at least one of resistance, capacitance, tunneling current, and phase.
7. A nanopore-based sequencing chip, comprising:
a nanopore array wafer defining a plurality of nanopores;
a top wafer bonded to a top side of the nanopore array wafer; and
a bottom wafer bonded to a bottom side of the nanopore array wafer, wherein the top wafer and the nanopore array wafer together define one or more nanofluidic channels, and the bottom wafer and the nanopore array wafer together define one or more microfluidic channels.
8. The nanopore-based sequencing chip of claim 7, wherein each of the plurality of nanopores is of a fixed identical size.
9. The nanopore-based sequencing chip of claim 7, further comprises:
a top driving electrode coupled to a bottom side of the top wafer;
a first set of sensing and biasing circuits fabricated on the top wafer, wherein the top driving electrode is electrically coupled to the first set of sensing and biasing circuits;
a bottom driving electrode coupled to a top side of the bottom wafer; and
a second set of sensing and biasing circuits fabricated on the bottom wafer, wherein the bottom driving electrode is electrically coupled to the second set of sensing and biasing circuits.
10. The nanopore-based sequencing chip of claim 8, further comprising:
a second top driving electrode embedded within the nanopore array wafer; and
a second bottom driving electrode embedded within the nanopore array wafer.
11. The nanopore-based sequencing chip of claim 8, further comprising:
a plurality of sensing electrodes embedded within the nanopore array wafer, each of the plurality of sensing electrodes abutting one of the plurality of nanopores.
12. A method to manufacture a nanopore-based sequencing chip usable in a portable molecule analyzer, comprising:
applying nanopantographic etch on a layer of conductive material deposited on a silicon substrate of a nanopore array wafer to define a plurality of nanopores on the nanopore array wafer;
bonding the nanopore array wafer to a bottom side of a top wafer to define one or more nanofluidic channels between the nanopore array wafer and the top wafer; and
bonding the nanopore array wafer to a top side of a bottom wafer to define one or more microfluidic channels between the nanopore array wafer and the bottom wafer.
13. The method of claim 12, further comprising:
fabricating a top driving electrode and a set of sensing and biasing circuits on the top wafer before bonding the top wafer to the nanopore array wafer.
14. The method of claim 12, further comprising:
fabricating a bottom driving electrode and a set of sensing and biasing circuits on the bottom wafer before bonding the bottom wafer to the nanopore array wafer.
15. The method of claim 12, further comprising:
directing a collimated monoenergetic ion beam at an array of submicro-diameter electrostatic lenses to define a plurality of nanometer features on the conductive layer on the silicon substrate of the nanopore array wafer,
wherein applying nanopantographic etch comprises applying a voltage on the layer of conductive material at which the plurality of nanometer features are defined such that the plurality of nanopores are formed at where the plurality of nanometer features are defined.
16. The method of claim 12, wherein a size of each of the plurality of nanopores is within a range of 1-nm to 200-nm.
17. A computer-readable storage medium embodying instructions that, when executed by a processing device, will cause the processing device to perform a method, the method comprising:
receiving measurement data from a nanopore-based sequencing chip in a portable molecule analyzer, wherein the measurement data is related to a sample of molecules input to the portable molecule analyzer; and
analyzing the measurement data to identify the sample of molecules substantially in real-time.
18. The computer-readable storage medium of claim 17, wherein the method further comprising:
retrieving data of a plurality of molecules from a database stored within the portable molecule analyzer; and
comparing result of the analyzing with the data of the plurality of molecules to identify the sample of molecules.
19. The computer-readable storage medium of claim 18, wherein the method further comprises:
storing result of the analyzing in the database for future reference.
20. The computer-readable storage medium of claim 18, wherein the method further comprises:
periodically downloading information from a remote source to update the database.
21. The computer-readable storage medium of claim 19, wherein the method further comprises:
wirelessly transmitting result of the analyzing from the portable molecule analyzer to a remote computing system.
22. The computer-readable storage medium of claim 19, wherein the method further comprises:
generating a graphical user interface (GUI) to be displayed on a display device of the portable molecule analyzer; and
displaying result of the analyzing in the GUI.
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Cited By (40)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130264206A1 (en) * 2012-04-09 2013-10-10 Samsung Electronics Co., Ltd. Biomolecule detection apparatus including plurality of electrodes
US20140019489A1 (en) * 2012-07-10 2014-01-16 Jinjun Wang Constructing Incremental Tree Model for Vein Image Recognition and Authentication
US20140113386A1 (en) * 2012-10-10 2014-04-24 Arizona Board Of Regents, Acting For And On Behalf Of Arizona State University Systems and devices for moleucle sensing and method of manufacturing thereof
US8771491B2 (en) 2009-09-30 2014-07-08 Quantapore, Inc. Ultrafast sequencing of biological polymers using a labeled nanopore
US8962242B2 (en) 2011-01-24 2015-02-24 Genia Technologies, Inc. System for detecting electrical properties of a molecular complex
US8986629B2 (en) 2012-02-27 2015-03-24 Genia Technologies, Inc. Sensor circuit for controlling, detecting, and measuring a molecular complex
US9041420B2 (en) 2010-02-08 2015-05-26 Genia Technologies, Inc. Systems and methods for characterizing a molecule
US9121059B2 (en) 2010-12-22 2015-09-01 Genia Technologies, Inc. Nanopore-based single molecule characterization
WO2015148127A1 (en) * 2014-03-25 2015-10-01 Genia Technologies, Inc. Nanopore-based sequencing chips using stacked wafer technology
EP2811292A4 (en) * 2012-01-30 2015-10-28 Univ Osaka Control method and control device for movement speed of substance, and use therefor
US20160010148A1 (en) * 2012-06-08 2016-01-14 Pacific Bioscience Of California, Inc. Identifying modified bases using hemi-natural nucleic acids
WO2016065339A1 (en) * 2014-10-24 2016-04-28 Quantapore, Inc. Efficient optical analysis of polymers using arrays of nanostructures
WO2016073318A1 (en) * 2014-11-05 2016-05-12 Genia Technologies, Inc. Exporting measurements of nanopore arrays
WO2016099672A1 (en) * 2014-12-18 2016-06-23 Genia Technologies, Inc. Printed electrode
EP3073264A1 (en) * 2015-03-25 2016-09-28 Robert Bosch Gmbh Sequencing device and method for operating a sequencing device
US20160301470A1 (en) * 2013-10-08 2016-10-13 Zte Corporation MIMO Visible Light Communication System Receiving Device
US9494554B2 (en) 2012-06-15 2016-11-15 Genia Technologies, Inc. Chip set-up and high-accuracy nucleic acid sequencing
US9506894B2 (en) 2012-12-27 2016-11-29 Quantum Biosystems Inc. Method for controlling substance moving speed and apparatus for controlling the same
US9535033B2 (en) 2012-08-17 2017-01-03 Quantum Biosystems Inc. Sample analysis method
US9551697B2 (en) 2013-10-17 2017-01-24 Genia Technologies, Inc. Non-faradaic, capacitively coupled measurement in a nanopore cell array
US9557294B2 (en) 2014-12-19 2017-01-31 Genia Technologies, Inc. Nanopore-based sequencing with varying voltage stimulus
US9605309B2 (en) 2012-11-09 2017-03-28 Genia Technologies, Inc. Nucleic acid sequencing using tags
US9605307B2 (en) 2010-02-08 2017-03-28 Genia Technologies, Inc. Systems and methods for forming a nanopore in a lipid bilayer
US9617595B2 (en) 2010-02-08 2017-04-11 Genia Technologies, Inc. Systems and methods for assembling a lipid bilayer on a substantially planar solid surface
US9644236B2 (en) 2013-09-18 2017-05-09 Quantum Biosystems Inc. Biomolecule sequencing devices, systems and methods
US9651539B2 (en) 2012-10-28 2017-05-16 Quantapore, Inc. Reducing background fluorescence in MEMS materials by low energy ion beam treatment
US9678055B2 (en) 2010-02-08 2017-06-13 Genia Technologies, Inc. Methods for forming a nanopore in a lipid bilayer
JP2017123838A (en) * 2016-12-14 2017-07-20 クオンタムバイオシステムズ株式会社 Controlling method and controlling apparatus for movement rate of material and uses thereof
US9759711B2 (en) 2013-02-05 2017-09-12 Genia Technologies, Inc. Nanopore arrays
US9862997B2 (en) 2013-05-24 2018-01-09 Quantapore, Inc. Nanopore-based nucleic acid analysis with mixed FRET detection
US9863904B2 (en) 2014-12-19 2018-01-09 Genia Technologies, Inc. Nanopore-based sequencing with varying voltage stimulus
US9885079B2 (en) 2014-10-10 2018-02-06 Quantapore, Inc. Nanopore-based polymer analysis with mutually-quenching fluorescent labels
US9903820B2 (en) 2007-05-08 2018-02-27 The Trustees Of Boston University Chemical functionalization of solid-state nanopores and nanopore arrays and applications thereof
WO2018109102A1 (en) * 2016-12-15 2018-06-21 F. Hoffmann-La Roche Ag Adaptive nanopore signal compression
US10126262B2 (en) 2015-09-24 2018-11-13 Genia Technologies, Inc. Differential output of analog memories storing nanopore measurement samples
KR101933619B1 (en) * 2011-12-26 2018-12-31 삼성전자주식회사 Nanopore device, method of fabricating the same, and DNA detection apparatus including the same
US10202644B2 (en) 2010-03-03 2019-02-12 Quantum Biosystems Inc. Method and device for identifying nucleotide, and method and device for determining nucleotide sequence of polynucleotide
WO2019060042A1 (en) * 2017-09-22 2019-03-28 Applied Materials, Inc. Method for simple fluidic addressing of a nanopore
US10261066B2 (en) 2013-10-16 2019-04-16 Quantum Biosystems Inc. Nano-gap electrode pair and method of manufacturing same
US10438811B1 (en) 2014-04-15 2019-10-08 Quantum Biosystems Inc. Methods for forming nano-gap electrodes for use in nanosensors

Families Citing this family (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2013042681A (en) * 2011-08-23 2013-03-04 Kyocer Slc Technologies Corp Wiring board for analyzing gene
EP2798055A4 (en) * 2011-12-28 2016-01-27 Agilent Technologies Inc Two dimensional nanofluidic ccd arrays for manipulation of charged molecules in solution
WO2014014696A2 (en) * 2012-07-16 2014-01-23 Genefluidics, Inc. Sample dependent selection of parameters for use in electrokinetic treatment of the sample
JP2014083045A (en) * 2012-10-26 2014-05-12 Kyocer Slc Technologies Corp Gene analysis wiring board and manufacturing method for the same
US20190154673A1 (en) 2016-07-29 2019-05-23 Selma Diagnostics Aps Improvements for methods in digital counting
US20190022647A1 (en) * 2016-02-22 2019-01-24 Hitachi, Ltd., Biological sample analysis chip, biological sample analyzer and biological sample analysis method
KR20190062514A (en) * 2016-10-03 2019-06-05 젠비다 테크놀로지 컴퍼니 리미티드 Apparatus and method for identification and analysis of molecules.
CN107090404B (en) * 2017-04-21 2019-08-13 京东方科技集团股份有限公司 A kind of gene sequencing chip and gene order surveying method, gene sequencing device
CN107377020B (en) * 2017-08-04 2019-09-17 深圳市梅丽纳米孔科技有限公司 The detection method of micro-fluidic chip and the biomarker based on micro-fluidic chip

Citations (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030040173A1 (en) * 2001-08-14 2003-02-27 The Penn State Research Foundation Fabrication of molecular scale devices using fluidic assembly
US20030136679A1 (en) * 2001-10-18 2003-07-24 The Board Of Trustees Of The University Of Illinois Hybrid microfluidic and nanofluidic system
US20040051154A1 (en) * 2002-09-12 2004-03-18 Mineo Yamakawa Microfluidic apparatus with integrated porous-substrate/sensor for real-time (bio)chemical molecule detection
US20040144658A1 (en) * 2003-01-27 2004-07-29 Flory Curt A. Apparatus and method for biopolymer indentification during translocation through a nanopore
US20050014162A1 (en) * 2003-07-17 2005-01-20 Barth Phillip W. Apparatus and method for threading a biopolymer through a nanopore
US20060275911A1 (en) * 2005-06-03 2006-12-07 Shih-Yuan Wang Method and apparatus for moleclular analysis using nanostructure-enhanced Raman spectroscopy
US20070131646A1 (en) * 2005-12-08 2007-06-14 University Of Houston Method and apparatus for nano-pantography
US7361313B2 (en) * 2003-02-18 2008-04-22 Intel Corporation Methods for uniform metal impregnation into a nanoporous material
US7741130B2 (en) * 2001-08-20 2010-06-22 President And Fellows Of Harvard College Fluidic arrays and method of using

Family Cites Families (46)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5795782A (en) 1995-03-17 1998-08-18 President & Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US6362002B1 (en) 1995-03-17 2002-03-26 President And Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US6267872B1 (en) 1998-11-06 2001-07-31 The Regents Of The University Of California Miniature support for thin films containing single channels or nanopores and methods for using same
US6465193B2 (en) 1998-12-11 2002-10-15 The Regents Of The University Of California Targeted molecular bar codes and methods for using the same
US6464842B1 (en) 1999-06-22 2002-10-15 President And Fellows Of Harvard College Control of solid state dimensional features
WO2000079257A1 (en) 1999-06-22 2000-12-28 President And Fellows Of Harvard College Molecular and atomic scale evaluation of biopolymers
US7582490B2 (en) 1999-06-22 2009-09-01 President And Fellows Of Harvard College Controlled fabrication of gaps in electrically conducting structures
US7258838B2 (en) 1999-06-22 2007-08-21 President And Fellows Of Harvard College Solid state molecular probe device
US6783643B2 (en) 1999-06-22 2004-08-31 President And Fellows Of Harvard College Control of solid state dimensional features
US6616895B2 (en) 2000-03-23 2003-09-09 Advanced Research Corporation Solid state membrane channel device for the measurement and characterization of atomic and molecular sized samples
US6413792B1 (en) 2000-04-24 2002-07-02 Eagle Research Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
AU7140101A (en) 2000-06-23 2002-01-08 Us Navy Microelectronic device and method for label-free detection and quantification ofbiological and chemical molecules
WO2002042496A2 (en) 2000-11-27 2002-05-30 The Regents Of The University Of California Methods and devices for characterizing duplex nucleic acid molecules
JP5025132B2 (en) 2002-10-29 2012-09-12 プレジデント・アンド・フェローズ・オブ・ハーバード・カレッジ Manufacture of carbon nanotube devices
US6905878B2 (en) 2002-12-19 2005-06-14 The Scripps Research Institute DNA array for high throughput solid-phase transfection and method for producing the same
US6806534B2 (en) * 2003-01-14 2004-10-19 International Business Machines Corporation Damascene method for improved MOS transistor
JP2006526777A (en) * 2003-02-28 2006-11-24 ブラウン ユニバーシティー Nanopores, methods for using them, methods for making them, and methods for characterizing biomolecules using them
WO2005017025A2 (en) * 2003-08-15 2005-02-24 The President And Fellows Of Harvard College Study of polymer molecules and conformations with a nanopore
US6846702B1 (en) 2003-10-24 2005-01-25 Agilent Technologies, Inc. Nanopore chip with N-type semiconductor
WO2005085233A1 (en) 2004-03-01 2005-09-15 The Government Of The United States Of America As Represented By Thesecretary Of The Navy Naval Research Laboratory Synthetic nanopores for dna sequencing
US7279337B2 (en) 2004-03-10 2007-10-09 Agilent Technologies, Inc. Method and apparatus for sequencing polymers through tunneling conductance variation detection
US7238485B2 (en) 2004-03-23 2007-07-03 President And Fellows Of Harvard College Methods and apparatus for characterizing polynucleotides
US20060210967A1 (en) 2004-07-02 2006-09-21 Agan Brian K Re-sequencing pathogen microarray
EP1784754A4 (en) 2004-08-13 2009-05-27 Harvard College An ultra high-throughput opti-nanopore dna readout platform
CN1309027C (en) * 2004-09-02 2007-04-04 上海交通大学 Nano etching method based on nano material disposition
US20060068401A1 (en) * 2004-09-30 2006-03-30 Flory Curt A Biopolymer resonant tunneling with a gate voltage source
US8563237B2 (en) * 2004-09-30 2013-10-22 Agilent Technologies, Inc. Biopolymer resonant tunneling with a gate voltage source
US7435353B2 (en) 2004-12-09 2008-10-14 President And Fellows Of Harvard College Patterning by energetically-stimulated local removal of solid-condensed-gas layers and solid state chemical reactions produced with such layers
US20060210995A1 (en) * 2005-03-15 2006-09-21 Joyce Timothy H Nanopore analysis systems and methods of using nanopore devices
AT529734T (en) 2005-04-06 2011-11-15 Harvard College Molecular characterization with carbon nanotube control
US20060231419A1 (en) 2005-04-15 2006-10-19 Barth Philip W Molecular resonant tunneling sensor and methods of fabricating and using the same
US20070048745A1 (en) 2005-08-30 2007-03-01 Joyce Timothy H Systems and methods for partitioned nanopore analysis of polymers
US20070178507A1 (en) 2006-01-31 2007-08-02 Wei Wu Method and apparatus for detection of molecules using nanopores
US20070298511A1 (en) 2006-04-27 2007-12-27 The Texas A&M University System Nanopore sensor system
US7777505B2 (en) 2006-05-05 2010-08-17 University Of Utah Research Foundation Nanopore platforms for ion channel recordings and single molecule detection and analysis
CN101495656B (en) 2006-06-07 2017-02-08 纽约哥伦比亚大学理事会 DNA sequencing by nanopore using modified nucleotides
US20080032290A1 (en) * 2006-08-03 2008-02-07 Young James E Nanopore flow cells
US20080280776A1 (en) 2006-12-04 2008-11-13 Rashid Bashir Method and apparatus for detection of molecules using a sensor array
GB0625070D0 (en) * 2006-12-15 2007-01-24 Imp Innovations Ltd Characterization of molecules
CN101225436A (en) * 2007-01-19 2008-07-23 深圳大学 Synthetic solid lateral nanometer pore
US8003319B2 (en) 2007-02-02 2011-08-23 International Business Machines Corporation Systems and methods for controlling position of charged polymer inside nanopore
KR101521990B1 (en) * 2007-04-04 2015-05-20 더 리젠츠 오브 더 유니버시티 오브 캘리포니아 Compositions, devices, systems, and methods for using a nanopore
US8192600B2 (en) 2007-09-27 2012-06-05 The Board Of Trustees Of The University Of Illinois Solid state device
JP5539210B2 (en) 2007-10-02 2014-07-02 プレジデント アンド フェローズ オブ ハーバード カレッジ Carbon nanotube synthesis for nanopore devices
US8273532B2 (en) 2007-10-02 2012-09-25 President And Fellows Of Harvard College Capture, recapture, and trapping of molecules with a nanopore

Patent Citations (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030040173A1 (en) * 2001-08-14 2003-02-27 The Penn State Research Foundation Fabrication of molecular scale devices using fluidic assembly
US7741130B2 (en) * 2001-08-20 2010-06-22 President And Fellows Of Harvard College Fluidic arrays and method of using
US20030136679A1 (en) * 2001-10-18 2003-07-24 The Board Of Trustees Of The University Of Illinois Hybrid microfluidic and nanofluidic system
US20040051154A1 (en) * 2002-09-12 2004-03-18 Mineo Yamakawa Microfluidic apparatus with integrated porous-substrate/sensor for real-time (bio)chemical molecule detection
US6806543B2 (en) * 2002-09-12 2004-10-19 Intel Corporation Microfluidic apparatus with integrated porous-substrate/sensor for real-time (bio)chemical molecule detection
US20040144658A1 (en) * 2003-01-27 2004-07-29 Flory Curt A. Apparatus and method for biopolymer indentification during translocation through a nanopore
US7361313B2 (en) * 2003-02-18 2008-04-22 Intel Corporation Methods for uniform metal impregnation into a nanoporous material
US20050014162A1 (en) * 2003-07-17 2005-01-20 Barth Phillip W. Apparatus and method for threading a biopolymer through a nanopore
US20060275911A1 (en) * 2005-06-03 2006-12-07 Shih-Yuan Wang Method and apparatus for moleclular analysis using nanostructure-enhanced Raman spectroscopy
US20070131646A1 (en) * 2005-12-08 2007-06-14 University Of Houston Method and apparatus for nano-pantography
US7883839B2 (en) * 2005-12-08 2011-02-08 University Of Houston Method and apparatus for nano-pantography

Cited By (65)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9903820B2 (en) 2007-05-08 2018-02-27 The Trustees Of Boston University Chemical functionalization of solid-state nanopores and nanopore arrays and applications thereof
US10101315B2 (en) 2007-05-08 2018-10-16 Trustees Of Boston University Chemical functionalization of solid-state nanopores and nanopore arrays and applications thereof
US9279153B2 (en) 2009-09-30 2016-03-08 Quantapore, Inc. Ultrafast sequencing of biological polymers using a labeled nanopore
US8771491B2 (en) 2009-09-30 2014-07-08 Quantapore, Inc. Ultrafast sequencing of biological polymers using a labeled nanopore
US9605307B2 (en) 2010-02-08 2017-03-28 Genia Technologies, Inc. Systems and methods for forming a nanopore in a lipid bilayer
US9678055B2 (en) 2010-02-08 2017-06-13 Genia Technologies, Inc. Methods for forming a nanopore in a lipid bilayer
US9041420B2 (en) 2010-02-08 2015-05-26 Genia Technologies, Inc. Systems and methods for characterizing a molecule
US10343350B2 (en) 2010-02-08 2019-07-09 Genia Technologies, Inc. Systems and methods for forming a nanopore in a lipid bilayer
US9377437B2 (en) 2010-02-08 2016-06-28 Genia Technologies, Inc. Systems and methods for characterizing a molecule
US10371692B2 (en) 2010-02-08 2019-08-06 Genia Technologies, Inc. Systems for forming a nanopore in a lipid bilayer
US10456993B2 (en) 2010-02-08 2019-10-29 Roche Sequencing Solutions, Inc. Systems and methods for forming a nanopore in a lipid bilayer
US9617595B2 (en) 2010-02-08 2017-04-11 Genia Technologies, Inc. Systems and methods for assembling a lipid bilayer on a substantially planar solid surface
US10202644B2 (en) 2010-03-03 2019-02-12 Quantum Biosystems Inc. Method and device for identifying nucleotide, and method and device for determining nucleotide sequence of polynucleotide
US9121059B2 (en) 2010-12-22 2015-09-01 Genia Technologies, Inc. Nanopore-based single molecule characterization
US9581563B2 (en) 2011-01-24 2017-02-28 Genia Technologies, Inc. System for communicating information from an array of sensors
US10156541B2 (en) 2011-01-24 2018-12-18 Genia Technologies, Inc. System for detecting electrical properties of a molecular complex
US8962242B2 (en) 2011-01-24 2015-02-24 Genia Technologies, Inc. System for detecting electrical properties of a molecular complex
KR101933619B1 (en) * 2011-12-26 2018-12-31 삼성전자주식회사 Nanopore device, method of fabricating the same, and DNA detection apparatus including the same
EP2811292A4 (en) * 2012-01-30 2015-10-28 Univ Osaka Control method and control device for movement speed of substance, and use therefor
US8986629B2 (en) 2012-02-27 2015-03-24 Genia Technologies, Inc. Sensor circuit for controlling, detecting, and measuring a molecular complex
US20130264206A1 (en) * 2012-04-09 2013-10-10 Samsung Electronics Co., Ltd. Biomolecule detection apparatus including plurality of electrodes
US9382575B2 (en) * 2012-04-09 2016-07-05 Samsung Electronics Co., Ltd. Biomolecule detection apparatus including plurality of electrodes
US20160010148A1 (en) * 2012-06-08 2016-01-14 Pacific Bioscience Of California, Inc. Identifying modified bases using hemi-natural nucleic acids
US10480027B2 (en) 2012-06-08 2019-11-19 Pacific Biosciences Of California, Inc. Nanopore sequencing methods
US9494554B2 (en) 2012-06-15 2016-11-15 Genia Technologies, Inc. Chip set-up and high-accuracy nucleic acid sequencing
US9436780B2 (en) * 2012-07-10 2016-09-06 Seiko Epson Corporation Constructing incremental tree model for vein image recognition and authentication
US20140019489A1 (en) * 2012-07-10 2014-01-16 Jinjun Wang Constructing Incremental Tree Model for Vein Image Recognition and Authentication
US9535033B2 (en) 2012-08-17 2017-01-03 Quantum Biosystems Inc. Sample analysis method
US20140113386A1 (en) * 2012-10-10 2014-04-24 Arizona Board Of Regents, Acting For And On Behalf Of Arizona State University Systems and devices for moleucle sensing and method of manufacturing thereof
US9274430B2 (en) * 2012-10-10 2016-03-01 Arizona Board Of Regents On Behalf Of Arizona State University Systems and devices for molecule sensing and method of manufacturing thereof
US10288599B2 (en) 2012-10-10 2019-05-14 Arizona Board Of Regents On Behalf Of Arizona State University Systems and devices for molecule sensing and method of manufacturing thereof
US9651539B2 (en) 2012-10-28 2017-05-16 Quantapore, Inc. Reducing background fluorescence in MEMS materials by low energy ion beam treatment
US9605309B2 (en) 2012-11-09 2017-03-28 Genia Technologies, Inc. Nucleic acid sequencing using tags
US9506894B2 (en) 2012-12-27 2016-11-29 Quantum Biosystems Inc. Method for controlling substance moving speed and apparatus for controlling the same
US9759711B2 (en) 2013-02-05 2017-09-12 Genia Technologies, Inc. Nanopore arrays
US10012637B2 (en) 2013-02-05 2018-07-03 Genia Technologies, Inc. Nanopore arrays
US9862997B2 (en) 2013-05-24 2018-01-09 Quantapore, Inc. Nanopore-based nucleic acid analysis with mixed FRET detection
US9644236B2 (en) 2013-09-18 2017-05-09 Quantum Biosystems Inc. Biomolecule sequencing devices, systems and methods
US20160301470A1 (en) * 2013-10-08 2016-10-13 Zte Corporation MIMO Visible Light Communication System Receiving Device
US10128945B2 (en) * 2013-10-08 2018-11-13 Zte Corporation MIMO visible light communication system receiving device
US10261066B2 (en) 2013-10-16 2019-04-16 Quantum Biosystems Inc. Nano-gap electrode pair and method of manufacturing same
US10466228B2 (en) 2013-10-16 2019-11-05 Quantum Biosystems Inc. Nano-gap electrode pair and method of manufacturing same
US10393700B2 (en) 2013-10-17 2019-08-27 Roche Sequencing Solutions, Inc. Non-faradaic, capacitively coupled measurement in a nanopore cell array
US9551697B2 (en) 2013-10-17 2017-01-24 Genia Technologies, Inc. Non-faradaic, capacitively coupled measurement in a nanopore cell array
US10006899B2 (en) 2014-03-25 2018-06-26 Genia Technologies, Inc. Nanopore-based sequencing chips using stacked wafer technology
WO2015148127A1 (en) * 2014-03-25 2015-10-01 Genia Technologies, Inc. Nanopore-based sequencing chips using stacked wafer technology
US10438811B1 (en) 2014-04-15 2019-10-08 Quantum Biosystems Inc. Methods for forming nano-gap electrodes for use in nanosensors
US9885079B2 (en) 2014-10-10 2018-02-06 Quantapore, Inc. Nanopore-based polymer analysis with mutually-quenching fluorescent labels
US9624537B2 (en) 2014-10-24 2017-04-18 Quantapore, Inc. Efficient optical analysis of polymers using arrays of nanostructures
WO2016065339A1 (en) * 2014-10-24 2016-04-28 Quantapore, Inc. Efficient optical analysis of polymers using arrays of nanostructures
US10429375B2 (en) 2014-11-05 2019-10-01 Roche Sequencing Solutions, Inc. Exporting measurements of nanopore arrays
WO2016073318A1 (en) * 2014-11-05 2016-05-12 Genia Technologies, Inc. Exporting measurements of nanopore arrays
US10060903B2 (en) 2014-11-05 2018-08-28 Genia Technologies, Inc. Exporting measurements of nanopore arrays
US9658190B2 (en) 2014-12-18 2017-05-23 Genia Technologies, Inc. Printed electrode
US20170284962A1 (en) * 2014-12-18 2017-10-05 Genia Technologies, Inc. Printed electrode
WO2016099672A1 (en) * 2014-12-18 2016-06-23 Genia Technologies, Inc. Printed electrode
EP3233268A4 (en) * 2014-12-18 2018-08-08 H. Hoffnabb-La Roche Ag Printed electrode
US9557294B2 (en) 2014-12-19 2017-01-31 Genia Technologies, Inc. Nanopore-based sequencing with varying voltage stimulus
US9863904B2 (en) 2014-12-19 2018-01-09 Genia Technologies, Inc. Nanopore-based sequencing with varying voltage stimulus
EP3073264A1 (en) * 2015-03-25 2016-09-28 Robert Bosch Gmbh Sequencing device and method for operating a sequencing device
US10160999B2 (en) 2015-03-25 2018-12-25 Robert Bosch Gmbh Sequencing device and method for operating a sequencing device
US10126262B2 (en) 2015-09-24 2018-11-13 Genia Technologies, Inc. Differential output of analog memories storing nanopore measurement samples
JP2017123838A (en) * 2016-12-14 2017-07-20 クオンタムバイオシステムズ株式会社 Controlling method and controlling apparatus for movement rate of material and uses thereof
WO2018109102A1 (en) * 2016-12-15 2018-06-21 F. Hoffmann-La Roche Ag Adaptive nanopore signal compression
WO2019060042A1 (en) * 2017-09-22 2019-03-28 Applied Materials, Inc. Method for simple fluidic addressing of a nanopore

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